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| Status |
Public on Jan 12, 2021 |
| Title |
Combined analysis of transcriptome and metabolome in tilapia (GIFT, Oreochromis niloticus) exposed to acute hypoxia stress |
| Organism |
Oreochromis niloticus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Dissolved oxygen (DO) in cultured water is one of the important environment factor in fish farming. Hypoxic environment affects fish growth, metabolism and immune system. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. In this study, the 96h median lethal hypoxia (96h-LH50) for Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) was first analyzed by linear interpolation. We built control (5mg/l) and hypoxic stress (96h-LH50) groups, and extracted the liver tissues for high-throughput transcriptome and metabolome sequencing. The identification and quantification results of metabolites showed that a total of 19656 metabolites had been obtained, of which 10390 were annotated. There were 3028 differentially expressed (DE) metabolites, of which 1596 metabolites were up-regulated and 1432 metabolites were down-regulated. We obtained 2375 DE genes, of which 1201 genes were up-regulated and 1174 genes were down-regulated. We verified 8 DE genes by quantitative real-time PCR. Our finding reveals the changes in metabolites and genes expression of GIFT and facilitate the understanding of regulatory pathways under hypoxic stress, which will help reduce the damage caused by hypoxic stress during culture.
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| Overall design |
A total of 90 experimental fish were used for the acute hypoxic stress experiment. Eighteen experimental fish were randomly placed in six tanks (3 fish per tank), three treatment tanks and three 5mg/L control tanks. The DO of the three treatment tanks was rapidly reduced to 0.7-0.8mg/L by pumping nitrogen into water from a nitrogen gas cylinder. Real-time reading with a DO meter were used to control the DO in water by adjusting oxygen intake. The sampling time was 96h. Three fish were taken from each tank and anesthetized with 200mg/L MS-222. The liver tissues were removed, divided into two parts, frozen in liquid nitrogen, and stored in -80℃. One part of liver was used to do high-throughput transcriptome and metabolome sequencing. The other part of the sample was used to analyze the expression levels of the genes at different DO by qRT-PCR
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| Contributor(s) |
Ma J, Qiang J, He J, Tao Y, Xu P, Bao J |
| Citation(s) |
33549051 |
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| Submission date |
Mar 01, 2020 |
| Last update date |
Feb 16, 2021 |
| Contact name |
Jun Qiang |
| E-mail(s) |
qiangj@ffrc.cn
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| Organization name |
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences
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| Street address |
9 Shanshi East road
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| City |
Wuxi |
| State/province |
Jiangsu |
| ZIP/Postal code |
214081 |
| Country |
China |
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| Platforms (1) |
| GPL26254 |
Illumina HiSeq 4000 (Oreochromis niloticus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA609548 |
| SRA |
SRP251173 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE146142_All_genes_fpkm_expression.xlsx |
3.7 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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